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I accidentally killed Heatran and I saved the game to challenge the elite four and defeat the champion, because I thought that's the only way to get legendaries back. But when I defeated the champion and all that again. He wasn't there. What happened? Was that my only chance to catch him?

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I read online that you should have been able to catch him again. Maybe try beating the Elite Four again and then coming back?
I did twice now and it still has t shown up. Do I have to wait a certain amount of time before I can recapture it?

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You can rematch Heatran after completing the Delta Episode and beating the Elite Four again. If you have already completed the Delta Episode, then you just need to beat the Elite Four. You should be able to do this any number of times, so you should be fine if you defeat a legendary Pokemon and forgot to save before you fought them.

Sources: This and knowledge.

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